Projects
Gigabyte-Scale Biological Sequence Alignment
An open-source SATA controller was integrated into a custom FPGA Accelerator implementation of the DIALIGN sequencing algorithm. Having FPGA device based access to large storage allows for lengthy query sequences to be aligned, without having to daisy-chain multiple FPGA devices.
The FPGA device is also connected via Ethernet to a Host PC to stream the required reference and query sequences.
Please see the poster that I presented at the Field-Programmable Technology (2014) conference for more details. The paper for this work, with the references to the open-source work, can be found here.